|
| Status |
Public on Jun 20, 2013 |
| Title |
WT_RNA-seq_Zt6_3 |
| Sample type |
SRA |
| |
|
| Source name |
WT_RNA-seq_Zt6
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
genotype/variation: wild type
age: adult
tissue: brain cortex
time of day: Zt+6
|
| Growth protocol |
B6(Cg)-Snord116tm1.1Uta/J (Snord116del) and WT C57BL/6J mice were obtained from Jackson Labs (Bar Harbor, ME) and housed in a 24-hour light/dark cycle (6am-6pm light, 6pm-6am dark), temperature controlled room and fed a standard diet of Picolab mouse chow 20 (PMI international, St. Louis, MO).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq: Mouse brain cortex was dissected on ice and placed in RNALater (Ambion). RNA was isolated using manufacturer's protocol for RNEasy Mini Kit (Qiagen part #:74101) following tissue homogenization with a Qiashredder (Qiagen part #: 79654).
For RNA-seq: Libraries were prepared according to Nugen's protocol accompanying the Encore Complete RNA-seq DR Multiplex system 1-8 (Part #: 0333-32). The libraries were analyzed on a Bioanalyzer, and submitted to the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley. Libraries were sequenced on the Hi-Seq 2000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 9
processed data file: RNAseq030113.txt (available on Series records)
|
| Data processing |
Basecalls performed using Illumina CASAVA_v1.8.0
RNA-seq reads were aligned to the mm9 genome assembly using TopHat v2.0.5 with options --library-type fr-firststrand -p 2 -G Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf
Differential transcript abundance was called using cuffdiff v2.0.2 with options -p 2 -L WT,Snord116del --FDR 0.05 -u --library-type fr-firststrand Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf.
Genome_build: mm9
Supplementary_files_format_and_content: Differential transcript abundance
|
| |
|
| Submission date |
Mar 01, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Weston Powell |
| E-mail(s) |
[email protected]
|
| Organization name |
UC Davis
|
| Department |
MMI
|
| Lab |
LaSalle Lab
|
| Street address |
3426 Tupper Hall
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE43575 |
A Prader-Willi locus lncRNA cloud modulates diurnal genes and energy expenditure. |
|
| Relations |
| SRA |
SRX246866 |
| BioSample |
SAMN01933041 |
